Transcription profiling of certolizumab pegol attenuation of the proinflammatory state in endothelial cells
ABSTRACT: Rheumatoid arthritis (RA) is associated with accelerated atherosclerosis and premature cardiovascular death. Anti-TNF therapy is thought to reduce clinical cardiovascular disease risk and improve vascular function in RA patients. However, the specific effects of TNF inhibitors on endothelial cell function are largely unknown. Our aim was to explore the effects of certolizumab pegol (CZP) on TNF-activated human aortic endothelial cells (HAoECs. HAoECs were cultured in vitro and exposed to i) TNF alone, ii) TNF plus CZP, or iii) neither agent followed by transcription profiling.
Project description:The aim of the experiment was to identify genes in the mouse suprachiasmatic nucleus whose expression was altered by exposure to a light pulse of 400 lux at CT16 (subjective night). C57BL/6 male mice were entrained to a 12:12 LD cycle and given a 30 min 400 lux light pulse at CT16. Punches of SCN tissue were collected at 30 (LP30), 60 (LP60)and 120 (LP120) mins after the start of the light pulse and flash frozen on dry ice. Sham SCN punches (Sham) were collected from mice not exposed to light at CT16. Total RNA from individual tissue samples was extracted using RNeasy micro kit from Qiagen using the lipid tissue protocol according to manufacturer's recommendations. Individual samples were analyzed for quality using an Agilent Bioanalzyer and only samples with a RIN of 8 and above were used. Samples were quantified by Nanodrop and 300ug of total RNA was used to prepare probes for hybridisation to Affymetrix Mouse Exon arrays. Probe preparation and array hybridisation was carried out according to Affymetrix protocols. Each array represents an individual SCN tissue punch.<br><br>
Project description:The experiment was to elucidate the association between copy number variation (CNV) and gene expression in colorectal cancer (CRC) samples and their corresponding non-cancerous tissues.
Project description:4 days old seedlings grown on MS without sucrose under continuous light of sco3-1 and Col have been used to extract RNA. Microarray analysis has been performed with three independent biological replicates<br>
Project description:Mouse bone marrow derived macrophages were stimulated with L3 larvae of the helminth Heligmosomoides polygyrus (Hp) (500 L3 /1 mio cells) in the presence or absence of immune serum (1:50 v:v) from challenge-Hp-infected mice.
Project description:Affymetrix Mouse Gene 1.0 ST hydridization using wt extracts from adult mice hearts as controls and Ts65Dn, Ms5Yah and Ts65Dn/Ms5Yah samples. <br><br>N = 5 mices per group of genotype.<br><br>Goal : assess the gene dosage effect on partial trisomic/monosomic mice modelling human Down syndrome.
Project description:Seeds were plated on sterilized membranes and grown under a 16h/8h light/dark regime at 21ﾰC. After 2 days of germination and 5 days of growth, the membrane was transferred to MS medium containing 0.3 ?g/ml bleomycin for 24 h. Triplicate batches of root meristem material seedlings were harvested for total RNA preparation.
Project description:Chromosomal instability is a hallmark of cancer and genes that display abnormal expression in chromosomally aberrant regions are likely to be key players in tumor progression. Identifying such driver genes from high-throughput data requires computational methods that are capable of integrating data from several sources and thereby enhance the reliability of driver gene identification. Hence, several algorithms that integrate copy number and expression data have been developed but their relative performance has not been assessed so far. We have compared 10 algorithms that integrate high-throughput copy number and transcriptomics data using simulated, cancer cell line and primary tumor data. Our results show that there are significant differences between the methods and their performance decreases significantly with small sample sets. Head and neck squamous cell carcinoma (HNSCC) cell lines from the tongue (UT-SCC-21,UT-SCC-24B, UT-SCC-30, UT-SCC-67, UT-SCC-73, UT-SCC-76A, UT-SCC-81, UT-SCC-87,UT-SCC-95) and larynx (UT-SCC-8, UT-SCC-11, UT-SCC-75) were provided by the Department of Otorhinolaryngology-Head and Neck Surgery at the Turku University Central Hospital (Turku, Finland). HNSCC cell lines SCC-4, SCC-9, SCC-25 and human skin keratinocyte HPV-16 E6/E7 transformed cell line CCD1106 KERTr was ordered from American Type Culture Collection (ATCC; Manassas, VA) and cultured according to the ATCC recommendations.